{
    "info": {
        "author": "Chris Sewell",
        "author_email": "chrisj_sewell@hotmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Scientific/Engineering :: Physics"
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        "description": "[![Build Status](https://travis-ci.org/chrisjsewell/aiida-crystal17.svg?branch=master)](https://travis-ci.org/chrisjsewell/aiida-crystal17)\n[![Coverage Status](https://coveralls.io/repos/github/chrisjsewell/aiida-crystal17/badge.svg?branch=master)](https://coveralls.io/github/chrisjsewell/aiida-crystal17?branch=master)\n[![Docs status](https://readthedocs.org/projects/aiida-crystal17/badge)](http://aiida-crystal17.readthedocs.io/) \n[![PyPI](https://img.shields.io/pypi/v/aiida-crystal17.svg)](https://pypi.python.org/pypi/aiida-crystal17/)\n\n# aiida-crystal17\n\nAiiDA plugin for running the [CRYSTAL17](http://www.crystal.unito.it/) code. \nThe code is principally tested against CRYSTAL17, \nbut the output parsing has also been tested against CRYSTAL14.\n\n**Documentation**: https://readthedocs.org/projects/aiida-crystal17\n\n## Installation\n\nTo install from pypi:\n\n```shell\n>> pip install aiida-crystal17\n```\n\nTo install the development version:\n\n```shell\n>> git clone https://github.com/chrisjsewell/aiida-crystal17 .\n>> cd aiida-crystal17\n>> pip install -e .  # also installs aiida, if missing (but not postgres)\n>> #pip install -e .[pre-commit,testing] # install extras for more features\n>> verdi quicksetup  # set up a new profile\n>> verdi calculation plugins  # should now show the calclulation plugins (with prefix crystal17.)\n```\n\n## Usage\n\n### Basic Calculation\n\nThe `crystal17.basic` is the simplest calculation plugin. \nIt takes a pre-written .d12 file as input \nand (optionally) a .gui file with geometry, for .d12 inputs containing the `EXTERNAL` keyword.\nAssuming AiiDA is configured and your database is running:\n\n```shell\n>> verdi daemon start         # make sure the daemon is running\n>> cd examples\n>> verdi run test_submit_basic.py       # submit test calculation\nsubmitted calculation; calc=Calculation(PK=5)\n>> verdi calculation list -a  # check status of calculation\n  PK  Creation    State           Sched. state    Computer    Type\n----  ----------  --------------  -------------  ----------  ---------------------------\n5     1m ago      WITHSCHEDULER                  localhost   crystal17.basic\n>> verdi calculation list -a  # after a few seconds\n  PK  Creation    State           Sched. state    Computer    Type\n----  ----------  --------------  -------------  ----------  ---------------------------\n5     1m ago      FINISHED        DONE           localhost   crystal17.basic\n```\n\nOnce the calculation has run, it will be linked to the input nodes and a number of output nodes:\n\n```shell\n>> verdi calculation show 5\n-----------  ---------------------------------------------------\ntype         CryBasicCalculation\npk           5\nuuid         3d9f804b-84db-443a-b6f8-69c15d96d244\nlabel        aiida_crystal17 test\ndescription  Test job submission with the aiida_crystal17 plugin\nctime        2018-08-27 15:23:38.670705+00:00\nmtime        2018-08-27 15:24:26.516127+00:00\ncomputer     [2] localhost\ncode         runcry17\n-----------  ---------------------------------------------------\n##### INPUTS:\nLink label       PK    Type\n---------------  ----  --------------\ninput_external   3     SinglefileData\ninput_file       4     SinglefileData\n##### OUTPUTS:\nLink label           PK  Type\n-----------------  ----  -------------\nremote_folder      6     RemoteData\nretrieved          7     FolderData\noutput_parameters  8     ParameterData\noutput_settings    9     StructSettingsData\noutput_structure   10    StructureData\n##### LOGS:\nThere are 1 log messages for this calculation\nRun 'verdi calculation logshow 5' to see them\n```\n\nThe outputs represent:\n\n-  ``remote_folder`` provides a symbolic link to the work directory\n   where the computation was run.\n-  ``retrieved`` stores a folder containing the full main output of\n   ``runcry17`` (as main.out)\n-  ``output_parameters`` stores a dictionary of key parameters in the\n   database, for later querying.\n-  ``output_structure`` stores the final geometry from the calculation\n-  ``output_settings`` stores additional information on the structure,\n    such as the symmetry operations.\n\nFor compatibility, parameters are named with the same convention as\n``aiida-quantumespresso``:\n\n.. code:: shell\n\n    >> verdi data parameter show 8\n    {\n      \"calculation_spin\": false, \n      \"calculation_type\": \"restricted closed shell\", \n      \"ejplugins_version\": \"0.9.7\", \n      \"energy\": -7380.22160519032, \n      \"energy_units\": \"eV\", \n      \"errors\": [], \n      \"mulliken_charges\": [\n        0.776999999999999, \n        -0.776999999999999\n      ], \n      \"mulliken_electrons\": [\n        11.223, \n        8.777\n      ], \n      \"number_of_assymetric\": 2, \n      \"number_of_atoms\": 2, \n      \"parser_class\": \"CryBasicParser\", \n      \"parser_version\": \"0.3.0a0\", \n      \"parser_warnings\": [\n        \"no initial structure available, creating new kinds for atoms\"\n      ], \n      \"scf_iterations\": 7, \n      \"volume\": 18.65461525, \n      \"wall_time_seconds\": 5, \n      \"warnings\": []\n    }\n\nYou can view the structure settings content by\n(use ``-c`` to view the symmetry operations):\n\n```shell\n>> verdi data cry17-settings show 9\ncentring_code: 1\ncrystal_type:  1\nnum_symops:    48\nspace_group:   1\n```\n\nThe final structure can be directly viewed by a number of different\nprograms (assuming the executables are available):\n\n```shell\n>> verdi data structure show --format xcrysden 10\n```\n\n### Main Calculation\n\nThe ``crystal17.main`` plugin is designed with a more programmatic\ninput interface. It creates the input ``.d12`` and ``.gui`` files,\nfrom a set of AiiDa nodes.\n\n```shell\n>> verdi daemon start         # make sure the daemon is running\n>> cd examples\n>> verdi run test_submit_main.py       # submit test calculation\nsubmitted calculation; calc=Calculation(PK=1)\n>> verdi calculation list -a  # check status of calculation\nPK  Creation    State           Sched. state    Computer       Type\n----  ----------  --------------  -------------  --------------  -----------------\n1     1m ago      WITHSCHEDULER   RUNNING        localhost-test  crystal17.main\n>> verdi calculation list -a  # after completion (~30 minutes if using runcry17)\nPK  Creation    State           Sched. state    Computer       Type\n----  ----------  --------------  -------------  --------------  -----------------\n1     4m ago      FINISHED        DONE           localhost-test  crystal17.main\n```\n\nOnce the calculation has run, it will be linked to the input nodes and a\nnumber of output nodes:\n\n```shell\nverdi calculation show 1\n-----------  ---------------------------------------------------\ntype         CryMainCalculation\npk           1\nuuid         3d9f804b-84db-443a-b6f8-69c15d96d244\nlabel        aiida_crystal17 test\ndescription  Test job submission with the aiida_crystal17 plugin\nctime        2018-08-27 15:23:38.670705+00:00\nmtime        2018-08-27 15:24:26.516127+00:00\ncomputer     [1] localhost-test\ncode         runcry17\n-----------  ---------------------------------------------------\n##### INPUTS:\nLink label      PK  Type\n------------  ----  -------------\nparameters    4     ParameterData\nsettings      5     StructSettingsData\nbasis_Ni      2     BasisSetData\nbasis_O       3     BasisSetData\nstructure     6     StructureData\n##### OUTPUTS:\nLink label           PK  Type\n-----------------  ----  -------------\nremote_folder      7     RemoteData\nretrieved          8     FolderData\noutput_parameters  9     ParameterData\noutput_structure   10    StructureData\n##### LOGS:\nThere are 1 log messages for this calculation\nRun 'verdi calculation logshow 1' to see them\n```\n\nThe inputs represent:\n\n-  `parameters` is a dictionary of (structure independent) data,\n    used to create the main.d12 file.\n-  `structure` stores the initial atomic configuration for the calculation.\n-  `settings` stores additional data related to the initial atomic\n    configuration, such as symmetry operations and initial spin.\n-  `basis_` store the basis set for each element.\n\n\n## Tests\n\nThe following will discover and run all unit test:\n\n```shell\n>> pip install -e .[testing]\n>> reentry scan -r aiida\n>> pytest -v\n```\n\nTo omit tests which call `runcry17`:\n\n```shell\n>> pytest -v -m \"not process_execution\"\n```\n\nor alternatively to call the `mock_runcry17` executable, \nfirst set the global environmental variable:\n\n```shell\n>> export MOCK_EXECUTABLES=true\n```\n\n## Development and Testing Notes\n\nThe original plugin template was created from the \n[aiida-plugin-cutter\n](https://github.com/aiidateam/aiida-plugin-cutter/tree/e614256377a4ac0c03f0ffca1dfe7bd9bb618983).\n\n### Coding Style Requirements\n\nThe code style is tested using [prospector](https://prospector.readthedocs.io/en/master/),\nwith the configuration set in `.prospector.yaml`, and [yapf](https://github.com/google/yapf).\n\nInstalling with `aiida-crystal17[pre-commit]` makes the [pre-commit](https://pre-commit.com/)\npackage available, which will ensure these tests are passed by reformatting the code \nand testing for lint errors before submitting a commit.\nIt can be setup by:\n\n```shell\n>> cd aiida-crystal17\n>> pre-commit install\n```\n\nOptionally you can run `yapf` and `prospector` separately:\n\n```shell\n>> yapf -r -i .  # recusivel find and format files in-place\n>> prospector \n```\n\nEditors like PyCharm also have automatic code reformat utilities, which should adhere to this standard.\n\n### Testing against mock CRYSTAL17 executables\n\nBecause CRYSTAL17 is a licensed software, it is not possible to source a copy of the executable on Travis CI.\nTherefore, a mock executable (`mock_runcry17`) has been created for testing purposes (which also speeds up test runs). \n\nThis executable computes the md5 hash of the supplied input file and tries to match it against a dictionary of \nprecomputed hashes. If found, the executable will write the matching output (from `test/output_files`) to stdout.\n\nTo use this mock executable when running tests, set the global variable `MOCK_EXECUTABLES=true`.\n\n### Setting up CRYSTAL17 locally\n\nTo set up local version of CRYSTAL17 on a mac (after downloading a copy from the distributor), I had to:\n\n1. Remove the quarantine from the executable permissions:\n\n    ```shell\n    xattr -c crystal \n    xattr -c properties\n    ```\n\n2. Create versions of the lapack/blas libraries in the expected folders:\n\n    ```shell\n    sudo port install lapack\n    sudo cp /opt/local/lib/lapack/liblapack.3.dylib /usr/local/opt/lapack/lib/liblapack.3.dylib\n    sudo cp /opt/local/lib/lapack/libblas.3.dylib /usr/local/opt/lapack/lib/libblas.3.dylib\n    ```\n\n3. Define environmental variables in `~/.bashrc`, as detailed in `cry17_scripts/cry17.bashrc`\n4. 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